5-60594451-A-G

Variant names:

• chr5-60594451-A-G
• rs4326096

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.735 in 150,396 control chromosomes in the GnomAD database, including 41,789 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.73 (41789 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.734 AC: 110367 AN: 150286 Hom.: 41728 Cov.: 27

Gnomad AFR AF: 0.932

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.721

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.735 AC: 110476 AN: 150396 Hom.: 41789 Cov.: 27 AF XY: 0.728 AC XY: 53365 AN XY: 73290

Gnomad4 AFR AF: 0.932

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.657

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.723

Alfa AF: 0.670 Hom.: 67750

Bravo AF: 0.749

Asia WGS AF: 0.671 AC: 2339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.57

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4326096; hg19: chr5-59890278;